Radiotherapy targeted to promote a systemic abscopal effect

ABSTRACT

Methods for personalized treatment of tumor lesions in subject with metastatic cancer are disclosed.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of U.S. Provisional Application No.61/975,573 filed Apr. 4, 2014, which is hereby incorporated herein byreference in its entirety.

BACKGROUND

Cancer is a heterogeneous group of malignant diseases that, in 2012,were responsible for more than 14% of deaths worldwide. Despite decadesof effort, most cancers remain incurable, which is largely due the stepchange from localized to metastatic disease. Transformed cancer cellsare confronted with an innate and adaptive immune surveillance, and itis believed that tumors that developed to become clinically apparenthave evolved to evade the immune system (Zitvogel L, et al. Nat RevImmunol. 2008 8(1):59-73). The notion of increasing the immune systemefficacy by therapeutic intervention in order to systemically eradicatecancer cells has long been a vision of oncologists and cancerresearchers. A particularly exciting development, hailed by the editorsof Science as the scientific breakthrough of 2013 (Couzin-Frankel J.Science. 2013 342(6165):1432-3), is that novel immunotherapeuticstrategies show remarkable responses in some patients, especially ifcombined with common cytotoxic agents. Radiotherapy and chemotherapeuticagents have been shown to substantially enhance tumor-specific immuneresponses in well-established tumors (Zitvogel L, et al. Nat RevImmunol. 2008 8(1):59-73; Reits E A, et al. J Exp Med. 2006203(5):1259-71; Lugade A A, et al. J Immunol. 2005 174(12):7516-23). Thesynergy between radiation and immunotherapy stems from radiation-induced(i) immunogenic cell death that locally exposes a wealth of tumorantigens, and (ii) release of stress proteins and danger associatedmolecular patterns (HSPs, DAMPs), which are endogenous immune adjuvantsthat can stimulate dendritic cell activation (Vatner R E, et al. FrontOncol. 2014 4:325) (FIG. 13C). Most fascinating is the observation thatthe stimulation of the immune system by localized radiotherapy maymodulate systemic regression of metastatic nodules, which is known asthe radiation-induced abscopal effect (Demaria S, et al. Int J RadiatOncol Biol Phys. 2004 58(3):862-70). Such abscopal responses triggeredby localized radiotherapy have been reported among others for lymphomas(Antoniades J, et al. Int J Radiat Oncol Biol Phys. 1977 2(1-2):141-7),renal cell carcinomas (Wersall P J, et al. Acta Oncol. 200645(4):493-7), papillary adenocarcinomas (Ehlers G, et al. Br J Radiol.1973 46(543):220-2), but given the large number of patients withmetastatic disease these reports remain considered anecdotal (Kaminski JM, et al. Cancer Treat Rev. 2005 31(3):159-72). Abscopal responses canbe triggered more reliably through combining irradiation withimmunotherapy (Vatner R E, et al. Front Oncol. 2014 4:325). A strongsystemic response against squamous cell carcinoma in mice was observedwhen dendritic cells where administered intratumorally after localirradiation (Akutsu Y, et al. Int J Oncol. 2007 31(3):509-15).

The possibility of rationally inducing abscopal affects usingradiotherapy and immunotherapy has the flavor of the long-sought “magicbullet.” But generation of the synergy required to provide local controland to induce the abscopal effect is difficult to predict due to myriadfactors including tumor and immune system heterogeneity as well as spaceand time dependent treatment effects. A wide range of mathematicalmodels has been developed to describe tumor immune interactions atdifferent phases of tumor progression (Kuznetsov V A, et al. Bull MathBiol. 1994 56(2):295-321; Wilkie K P. Adv Exp Med Biol. 2013 734:201-34;d'Onofrio A, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2011 84(3Pt 1):031910), or to look at different pathways that are or could beexploited for immunotherapy (Arciero J C, et al. Discret Contin Dyn S.2004 4(1):39-58; Kirchner D, et al. J Math Biol. 1998 37(3):235-52;Kronik N, et al. PloS one. 2010 5(12):e15482; Kronik N, et al. CancerImmunol Immunother. 2008 57(3):425-39; Cappuccio A, et al. Cancer Res.2006 66(14):7293-300), but all focused on a single tumor site. Thus, noprominent inroads have been made to decipher immune-modulated systemicmetastatic response triggered by localized radiotherapy.

SUMMARY

Methods for personalized treatment of tumor lesions in subject withmetastatic cancer or multiple primary tumors are disclosed. For example,for a subject having a plurality of tumor lesions in two or more organs,the method can be used to select a tumor lesion and/or tumor bearingorgan that has the highest chance of producing a systemic abscopaleffect after treatment with a localized therapy that induces immunogeniccell death, which triggers an immune response.

In some embodiments, the method involves determining the location andvolume for each of the plurality of tumor lesions in the subject. Forexample, this can involve three-dimensional radiological images of thesubject registering geographic locations of each of the plurality oftumor lesions. Non-limiting examples of radiological images that can beused to determine location and/or volume of a tumor lesion includepositron emission tomography (PET) scans, x-ray computerized tomography(CT), magnetic resonance imaging (MRI), nuclear magnetic resonanceimaging (NMRI), magnetic resonance tomography (MRT), or a combinationthereof.

In some embodiments, the method further involves modeling the blood flowdynamics and T cell infiltration probabilities in a single cardiac cyclefor each tumor lesion to predict systemic distribution of T cellsactivated at each tumor lesion. For example, this step can involvecomparing the volume of each tumor lesion to the volume of its tumorbearing organ; determining a physiologic blood flow fraction for eachtumor bearing organ; calculating for each tumor lesion an infiltrationprobability that predicts whether a T cell in circulation willinfiltrate the tumor lesion in a single circulatory cycle based on thepercent of organ taken, the physiologic blood flow fraction of the tumorlesion or the tumor bearing organ, and the extravasation probability forT cells activated in the organ of the tumor lesion, not activated in theorgan of the tumor lesion, or a combination thereof; calculating foreach tumor lesion a homing probability that predicts the relative numberof activated T cells that will home to the tumor lesion based on theinfiltration probabilities for each tumor lesion; and calculating foreach tumor lesion a homing distribution entropy value that predicts therelative distribution of T cells activated in the tumor lesion based onthe total number of tumor lesions and the calculated homing probabilityfor each tumor lesion.

In some embodiments, the method further involves calculating animmunogenicity index value for each tumor lesion based on the predictedhoming distribution and volume of each tumor lesion relative to thelargest tumor lesion. This immunogenicity index value can predict forwhich tumor lesion there is a largest likelihood that a local therapythat induces immunogenic cell death in a subject of the tumor lesionwill induce a systemic abscopal effect. For example, a large tumor thathas non-uniform homing distribution, and a small tumor that has close touniform homing distribution to each organ compartment would both havelower immunogenicity indexes compared to a large tumor that has close touniform homing distribution to each tumor bearing organ compartment.

For example, the method can further involve irradiating the tumorlesion(s) in the subject having the highest immunogenicity index. Forexample, the tumor lesion(s) can be treated with fractionated radiationtherapy, hypofractionated radiation therapy, hyperfractionated radiationlesion therapy, single-dose irradiation, stereotactic radiosurgery, orstereotactic body radiation therapy.

The method can also involve the use of an ablative therapy of the tumorlesion(s) having the highest immunogenicity index. Ablative cancertreatments use either heat or cold to destroy, or ablate, cancer tumorswithout the need for more invasive surgery. Non-limiting examples ofablative therapy include thermal ablation (radiofrequency ablation(RFA), microwave ablation, and non-invasive high intensity focusedultrasound (HIFU) ablation.

The method can also involve the use of local chemotherapeutics throughintratumoral administration of chemotherapy, chemotherapy deliveredthrough nanoparticles, or hypoxia-activated prodrugs (HAP). Non-limitingexamples of HAP are drug candidates AQ4N (Novacea), PR-104 (Proacta) andTH-302 (Threshold Pharmaceuticals).

The method can also involve treating the subject with local or systemicimmunotherapy, chemotherapy, or combination thereof. For example, themethod can further involve intratumoral injection of dendritic cellsinto the tumor lesion(s) having the highest immunogenicity index.

The disclosed methods can be used in any subject with two or more tumorlesions in different organs to identify the best organ to treat andpotentially induce an abscopal effect that treats the remaining tumorlesions. In some cases, at least one of the tumor lesions is ametastatic tumor lesion. However, the method can also be used when oneor more of the tumor lesions are primary tumors.

In some cases, at least one of the tumor lesions must be treated by alocal therapy that induces immunogenic cell death, such as radiotherapy,for medical reasons independent of the desire to promote an abscopaleffect. In these cases, the method accounts for this and identifiestumor lesion(s) in the subject having the highest immunogenicity indexin view of the preselected tumor lesion. In some cases, this involvesidentifying tumor lesions having complementarity in homing distributionvalues with that of the preselected tumor lesion. For example, a tumorthat is predicted to home only to the liver may have the highestimmunogenicity index when treated in combination with a preselectedtumor lesion that homes to every organ compartment other than the liver.

In some cases, multiple tumor lesions may be treated by local therapythat induces immunogenic cell death, such as radiotherapy. In thesecases, the method accounts for this and identifies tumor lesion(s) inthe subject having the highest immunogenicity index in combination. Insome cases, this involves identifying tumor lesions havingcomplementarity in homing distribution values with that of thepreselected tumor lesion

In some cases, local treatment induced systemic immune response may leadto eradication of circulating tumor cells or un-detectablemicro-metastases in different organs.

The disclosed method can also take into account the maximum therapydosage that each tumor lesion and tumor bearing organ can receive, e.g.,due to potential complications in surrounding tissue. This “doseability”can therefore be used in some embodiments to affect the immunogenicityscore of the lesion, or possibly disqualify the tumor lesion altogether.In addition, coupling “doseability” with the immunogenicity index mightshow that in some cases it is better to irradiate two lesions with low“doseability” than one highly “dosable” alone.

Also disclosed is a system for providing a personalized treatment planfor a subject with a plurality of tumor lesions in two or more tumorbearing organs. The system generally comprises a memory operably coupledto the processor, wherein the memory has computer-executableinstructions stored thereon that, when executed by the processor, causethe processor to: determine a respective volume of each of the tumorlesions using at least one possibly manually pre-processed radiologicalimage of the subject; obtain a respective physiologic blood flowfraction associated with each of the tumor bearing organs or directlytumor lesions; obtain a respective T cell extravasation probabilityassociated with each of the tumor lesions; calculate a respective homingdistribution for each of the tumor lesions based on the respectivevolume of each of the tumor lesions, the respective physiologic bloodflow fraction associated with each of the tumor lesions, and therespective T cell extravasation probability associated with each of thetumor lesions; calculate a respective immunogenicity index value foreach of the tumor lesions based on the respective volumes of each of thetumor lesions and the respective homing distributions for each of thetumor lesions; and provide a recommendation for treating one or more ofthe tumor bearing organs with a therapy that induces immunogenic celldeath based on the respective immunogenicity index values for each ofthe tumor lesions. In some cases, the memory has furthercomputer-executable instructions stored thereon that, when executed bythe processor, cause the processor to receive at least one radiologicalimage or the complete radiological data set of the subject.

Non-limiting examples of radiological images that can be used includepositron emission tomography (PET) scans, x-ray computer tomography, ora combination thereof.

In some embodiments, calculating the respective homing distribution foreach of the tumor lesions comprises calculating a respectiveinfiltration probability for each of the tumor lesions that predictswhether a T cell in circulation will infiltrate each of the tumorlesions in a single circulatory cycle, and wherein the respectiveinfiltration probability for each of the tumor lesions is based on therespective volume of each of the tumor lesions, the respectivephysiologic blood flow fraction associated with each of the tumorlesions, and the respective T cell extravasation probability associatedwith each of the tumor lesions.

In some embodiments, calculating the respective homing distribution foreach of the tumor lesions comprises calculating a respective homingprobability for each of the tumor lesions that predicts the fraction ofactivated T cells that will home to each of the tumor lesions, andwherein the respective homing probability for each of the tumor lesionsis based on the respective infiltration probability for each of thetumor lesions.

In some embodiments, calculating the respective homing distribution foreach of the tumor lesions comprises calculating a respective homingdistribution entropy value for each of the tumor lesions that predictsthe relative distribution of T cells activated in each of the tumorlesions, and wherein the respective homing distribution entropy valuefor each of the tumor lesions is based on a total number of the tumorlesions and the respective homing probability for each of the tumorlesions.

In some embodiments, the respective immunogenicity index value for eachof the tumor lesions is based on the respective homing distributionentropy value for each of the tumor lesions and the respective volume ofeach of the tumor lesions.

In some embodiments, the respective T cell extravasation probabilitycomprises a probability of T cells activated in a tumor bearing organ ofeach of the tumor lesions, not activated in the tumor bearing organ ofeach of the tumor lesions, or a combination thereof.

In some embodiments, the memory has further computer-executableinstructions stored thereon that, when executed by the processor, causethe processor to calculate a respective volume ratio of: (i) therespective volume of each of the tumor lesions to (ii) a volume of atumor bearing organ of each of the tumor lesions, wherein the respectivevolume ratio for each of the tumor lesions is used in the calculation ofthe respective immunogenicity index value for each of the tumor lesions.

In some embodiments, the memory has further computer-executableinstructions stored thereon that, when executed by the processor, causethe processor to calculate a respective blood flow fraction ratio of:(i) the respective physiologic blood flow fraction associated with eachof the tumor lesions to (ii) a respective physiologic blood flowfraction associated with a compartment of each of the tumor lesions,wherein the respective blood flow fraction ratio for each of the tumorlesions is used in the calculation of the respective immunogenicityindex value for each of the tumor lesions.

In some embodiments, the respective immunogenicity index values for eachof the tumor lesions predicts which of the lesions has the highestlikelihood that treating each of the tumor lesions with a targetedtherapy that induces immunogenic cell death will induce an abscopaleffect. For example, the recommendation can be to treat a tumor bearingorgan with the highest likelihood of inducing the abscopal effect. Asanother example, the recommendation can be to treat a plurality of tumorbearing organs with the combined highest likelihood of inducing theabscopal effect.

In some embodiments, the memory has further computer-executableinstructions stored thereon that, when executed by the processor, causethe processor to consider a first preselected tumor bearing organ as anecessary target for treatment and provide a recommendation forirradiating a second tumor bearing organ having tumor lesions with thehighest immunogenicity index in view of a preselected tumor bearingorgan.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

FIG. 1 shows images of pre- and post-treatment PET of a patient withmetastatic melanoma. Two liver lesions (arrow) were treated withradiation therapy (20 Gy/fraction) followed by systemic high-dose IL-2.

FIG. 2 is a diagram of a research design to make treatmentrecommendations and predict the likelihood of abscopal effects.

FIG. 3 shows the translation of radiological diagnostic scans into a‘virtual patient’ interconnected metastatic-lymphatic network.

FIG. 4 shows spatio-temporal propagation of immune signals from singleirradiated lymph nodes.

FIG. 5 is a proposed mathematical model of the interplay between Tumor(TN+TI) and Immune (R+E) populations and perturbation during radiationand immunotherapy.

FIGS. 6A to 6C show simulation results reproducing clinical tumor growthand T cell dynamics of responders (FIG. 6A, 6C) and nonresponders (FIG.6B). The patient in FIG. 6C was a non-responder that became a responderwith modified immunotherapy schedule.

FIG. 7 provides framework results. Shown on the left is apatient-specific interconnected metastatic-lymphatic network. Metastases(blue) and lymph nodes (red) connected through the shortest paths. Showncenter is the deviation of the global impact each tumor side has on theentire lymphatic network, and the likelihood of achieving an abscopaleffect dependent on irradiated tumor site. Shown on the right aresimulation results of patient-specific treatment. Abscopal effectachieved by irradiating tumor site ID 10 as observed clinically.Irradiation of tumor side ID 17 with little global impact yields localcontrol but systemic progression.

FIG. 8 is a diagram showing integration of the quantitative frameworkinto the clinical protocol and high-resolution spatio-temporal cancerimmunological data acquisition.

FIG. 9 shows equations for a multiscale model of lymph nodes andmetastasis.

FIGS. 10A to 10C are schematics of the interplay between tumor andimmune populations without treatment (FIG. 10A), with radiation therapy(FIG. 10B), and with immunotherapy (FIG. 10C).

FIG. 11 is a proposed mathematical model of the interplay betweentolerogenic T cells, immunogenic T cells, effector T cells, and Tregs.

FIG. 12 is a diagram a representative protocol.

FIGS. 13A to 13C illustrate the process of activated T cell trafficking.FIG. 13A depicts activated cytotoxic T cell (CTL) entering the bloodsystem via great veins, flowing through the pulmonary circulation, andthen going into systemic circulation. Venous blood from gastrointestinaltract and spleen goes to the liver through hepatic portal vein. FIG. 13Billustrates that in each compartment CTL can flow through withoutreaching the tumor site or enter one of metastatic sites (circles) andextravasate into the tissue. FIG. 13C illustrates how radiotherapy (RT)triggers immunogenic cells that activate dendritic cells (DCs) that thentravel to lymph nodes. DCs transform naïve T cells into CTLs, which, incase of non-metastatic disease, travel back through the blood system tothe tumor site to exert their cytotoxic effects.

FIGS. 14A to 14C show T cells homing distribution for differentactivation sites and extravasation probabilities. Model predicted homingdistributions between metastatic sites present in the first consideredvirtual case study comprised of breast (113 cc), liver (220 cc) and lung(270 cc) metastases for different sites of activation breast (FIG. 14A),liver (FIG. 14B), lung (FIG. 14C) and for different values ofextravasation probabilities h_(n) and h_(a). Rectangles correspond tothe narrow ranges around estimated value of h_(n)/h_(a). FIG. 14D showsthe average number of transitions between model compartments beforeextravasation at one of the metastatic sites for different sites ofactivation and different extravasation probabilities h_(n) and h_(a).Calculations were performed using parameters reported in Table 2.

FIGS. 15A to 15B show comparison of normalized entropy values (FIG. 15A,eqn. (D)), and immunogenicity indices (FIG. 15B, eqn. (E)), between themetastatic sites present in the first considered case study comprised ofbreast (113 cc), liver (220 cc) and lung (270 cc) metastases fordifferent extravasation probabilities h_(n) and h_(a). FIG. 15C showsresults of the analysis of other 40 virtual case studies of possiblemetastatic tumors in lung, liver, kidney and the breast. Circles denoteexistence of the metastatic site and radius corresponds to the tumorsize. Black background highlights the tumor with the highestimmunogenicity index for h_(n)/h_(a)=⅓ and h_(a)=0.6. Calculations wereperformed using parameters reported in Table 2.

FIGS. 16A to 16B show model predicted growth of the primary breast tumorbefore and after onset of lung metastasis (FIG. 16A) together withcorresponding number of infiltrating T cells (FIG. 16B). FIGS. 16C and16D show dynamics patterns of T cells homing probabilities when T cellsare activated in response to the breast tumor (FIG. 16C) and lungmetastasis (FIG. 16D). Simulations were performed with h_(a)=0.6,h_(n)=0.2, and parameters reported in Tables 1 and 2, under additionalassumption that the lung tumor has twice the nominal growth rate.

FIGS. 17A and 17B show that model predicted dynamics of the number ofcancer cells (FIG. 17A) and effector to cancer cells ratio (FIG. 17B) inlung metastasis after surgical removal of the breast tumor and localeffector cells at day 400. Simulations were performed with h_(a)=0.6,h_(n)=0.2, and parameters reported in Tables 1 and 2, under additionalassumption that the lung tumor has twice the nominal growth rate.

FIG. 18 is a flowchart depicting an example process for calculating animmunogenicity score for each tumor site that predicts the optimalsite(s) for radiation therapy to promote an abscopal effect.

FIG. 19 is an example computing device that can be configured to performoperations described herein.

DETAILED DESCRIPTION

Disclosed herein is a tumor-immune system interactions modelingframework that incorporates a mathematical model of activated T celltrafficking between metastatic sites. As disclosed herein, an abscopalresponse can be achieved when T cells that are locally activated byradiotherapy (or any other treatment inducing immunogenic cell death)are systemically distributed among the metastatic sites in numberssufficient to tip immune surveillance back in favor of tumor eradiationat each metastatic site. Trafficking and distribution of activated Tcells are shown to strongly depend on the geographic distribution ofmetastatic sites, physiologic blood flow fractions to tumor bearingorgans, tumor burden in each metastatic tissue, and the strength ofimmune cell homing cues. Different metastatic sites may have varyingpotential to trigger a systemic response. On the basis of the T cellhoming distribution optimum treatment targets were determined in avirtual clinical trial. A model of tumor-immune interactions wasincorporated into the framework to simulate local tumor growth of eachmetastasis. This provides insights into the tumor growth and treatmentresponse dynamics.

FIG. 18 is a flowchart depicting an example process for calculating animmunogenicity score for each tumor site that predicts the optimalsite(s) for radiation therapy to promote an abscopal effect.

The cancer of the disclosed methods can be any cell in a subjectundergoing unregulated growth, invasion, or metastasis. In some aspects,the cancer can be any neoplasm or tumor for which radiotherapy iscurrently used. Alternatively, the cancer can be a neoplasm or tumorthat is not sufficiently sensitive to radiotherapy using standardmethods. Thus, the cancer can be a sarcoma, lymphoma, leukemia,carcinoma, blastoma, or germ cell tumor. A representative butnon-limiting list of cancers that the disclosed compositions can be usedto treat include lymphoma, B cell lymphoma, T cell lymphoma, mycosisfungoides, Hodgkin's Disease, myeloid leukemia, bladder cancer, braincancer, nervous system cancer, head and neck cancer, squamous cellcarcinoma of head and neck, kidney cancer, lung cancers such as smallcell lung cancer and non-small cell lung cancer,neuroblastoma/glioblastoma, ovarian cancer, pancreatic cancer, prostatecancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas ofthe mouth, throat, larynx, and lung, colon cancer, cervical cancer,cervical carcinoma, breast cancer, epithelial cancer, renal cancer,genitourinary cancer, pulmonary cancer, esophageal carcinoma, head andneck carcinoma, large bowel cancer, hematopoietic cancers; testicularcancer; colon and rectal cancers, prostatic cancer, and pancreaticcancer.

This disclosed method can be used to predict which of the lesion has thehighest likelihood that a targeted therapy that induces immunogenic celldeath in a subject of the tumor lesion will induce an abscopal effect.Targeted therapies used to induce cytoimmunogenic cell death in tumorsinclude radiotherapy and ablative therapies. Ablative cancer treatmentsuse either heat or cold to destroy, or ablate, cancer tumors without theneed for more invasive surgery. Non-limiting examples of ablativetherapy include thermal ablation (radiofrequency ablation (RFA),microwave ablation, and non-invasive high intensity focused ultrasound(HIFU) ablation.

Radiation therapy, radiotherapy, or radiation oncology is therapy usingionizing radiation, generally as part of cancer treatment to control orkill malignant cells. Radiation may be prescribed by a radiationoncologist for curative, adjuvant, neoadjuvant, therapeutic, orpalliative treatment. It is also common to combine radiation therapywith surgery, chemotherapy, hormone therapy, immunotherapy or somemixture of the four. Most common cancer types can be treated withradiation therapy in some way. The precise treatment intent (curative,adjuvant, neoadjuvant, therapeutic, or palliative) will depend on thetumor type, location, and stage, as well as the general health of thepatient. Total body irradiation (TBI) is a radiation therapy techniqueused to prepare the body to receive a bone marrow transplant. However,the disclosed methods generally involve the use of targeted, localizedradiation therapy to promote an abscopal effect. Brachytherapy, in whicha radiation source is placed inside or next to the area requiringtreatment, is another form of radiation therapy that minimizes exposureto healthy tissue during procedures to treat cancers of the breast,prostate and other organs.

The amount of radiation used in photon radiation therapy is measured ingray (Gy), and varies depending on the type and stage of cancer beingtreated. For curative cases, the typical dose for a solid epithelialtumor ranges from 60 to 80 Gy, while lymphomas are treated with 20 to 40Gy. Preventive (adjuvant) doses are typically around 45-60 Gy in 1.8-2Gy fractions (for breast, head, and neck cancers.) Many other factorsare considered by radiation oncologists when selecting a dose, includingwhether the patient is receiving chemotherapy, patient comorbidities,whether radiation therapy is being administered before or after surgery,and the degree of success of surgery.

Delivery parameters of a prescribed dose are determined during treatmentplanning (part of dosimetry). Treatment planning is generally performedon dedicated computers using specialized treatment planning software.Depending on the radiation delivery method, several angles or sourcesmay be used to sum to the total necessary dose. The planner will try todesign a plan that delivers a uniform prescription dose to the tumor andminimizes dose to surrounding healthy tissues.

The total dose is fractionated (spread out over time) for severalimportant reasons. Fractionation allows normal cells time to recover,while tumor cells are generally less efficient in repair betweenfractions. Fractionation also allows tumor cells that were in arelatively radioresistant phase of the cell cycle during one treatmentto cycle into a sensitive phase of the cycle before the next fraction isgiven. Similarly, tumor cells that were chronically or acutely hypoxic(and therefore more radioresistant) may reoxygenate between fractions,improving the tumor cell kill.

In North America, Australia, and Europe, the standard fractionationschedule for adults is 1.8 to 2 Gy per day, five days a week. In somecancer types, prolongation of the fraction schedule over too long canallow for the tumor to begin repopulating, and for these tumor types,including head-and-neck and cervical squamous cell cancers, radiationtreatment is preferably completed within a certain amount of time. Forchildren, a typical fraction size may be 1.5 to 1.8 Gy per day, assmaller fraction sizes are associated with reduced incidence andseverity of late-onset side effects in normal tissues.

In some cases, two fractions per day are used. This schedule, known ashyperfractionation, is used on tumors that regenerate more quickly whenthey are smaller. In particular, tumors in the head-and-neck demonstratethis behavior. One fractionation schedule that is increasingly beingused and continues to be studied is hypofractionation. This is aradiation treatment in which the total dose of radiation is divided intolarge doses. Typical doses vary significantly by cancer type, from 2.2Gy/fraction to 20 Gy/fraction. The logic behind hypofractionation is tolessen the possibility of the cancer returning by not giving the cellsenough time to reproduce and also to exploit the unique biologicalradiation sensitivity of some tumors. One commonly treated site wherethere is very good evidence for such treatment is in breast cancer.

One of the best-known alternative fractionation schedules is ContinuousHyperfractionated Accelerated Radiation therapy (CHART). CHART, used totreat lung cancer, consists of three smaller fractions per day. Althoughreasonably successful, CHART can be a strain on radiation therapydepartments.

Another increasingly well-known alternative fractionation schedule, usedto treat breast cancer, is called Accelerated Partial Breast Irradiation(APBI). APBI can be performed with either brachytherapy or with externalbeam radiation. APBI normally involves two high-dose fractions per dayfor five days, compared to whole breast irradiation, in which a single,smaller fraction is given five times a week over a six-to-seven-weekperiod. An example of APBI where the entire dose is delivered in asingle fraction is TARGIT.

The methods provided herein can be performed with any suitableradiotherapy, including, but not limited to, external beam radiotherapy,also known as teletherapy; sealed source radiotherapy, also known asbrachytherapy; unsealed source radiotherapy; radioisotope therapy; andradioimmunotherapy.

In some embodiments, the radiotherapy is external radiation therapy.Examples of external radiation therapy include, but are not limited to,conventional external beam radiotherapy; three-dimensional conformalradiation therapy (3D-CRT), which delivers shaped beams to closely fitthe shape of a tumor from different directions; intensity modulatedradiation therapy (IMRT), e.g., helical tomotherapy, which shapes theradiation beams to closely fit the shape of a tumor and also alters theradiation dose according to the shape of the tumor; conformal protonbeam radiation therapy; image-guided radiotherapy (IGRT), which combinesscanning and radiation technologies to provide real time images of atumor to guide the radiation treatment; intraoperative radiation therapy(IORT), which delivers radiation directly to a tumor during surgery;stereotactic radiosurgery, which delivers a large, precise radiationdose to a small tumor area in a single session; hyperfractionatedradiotherapy, e.g., continuous hyperfractionated acceleratedradiotherapy (CHART), in which more than one treatment (fraction) ofradiotherapy are given to a subject per day; and hypofractionatedradiotherapy, in which larger doses of radiotherapy per fraction isgiven but fewer fractions.

In another embodiment, the radiotherapy is internal radiation therapy.Example of internal radiation therapy include, but are not limited to,interstitial, intracavitary, intraluminal, intravenously radiationtherapy, and implant radiation therapy, such as implantation ofradioactive beads, particles, or seeds. In some embodiments, theradiotherapy is sealed source radiotherapy. In another embodiment, theradiotherapy is unsealed source radiotherapy.

In yet another embodiment, the radiotherapy is radioisotope therapy orradioimmunotherapy, where the radiotherapy is performed by administeringa radioisotope parenterally to a subject, e.g., by injecting to asubject a tumor-specific antibody-radioisotope conjugate. Suitableradioisotopes for radioisotope therapy or radioimmunotherapy include,but are not limited to, ⁷²As, ¹⁹⁸Au, ²⁰⁶Bi, ⁷⁷Br, ¹¹C, ¹⁴C, ⁴⁷Ca, ¹²⁹Ce,¹³⁷Ce, ⁵⁵Co, ⁵⁶Co, ⁵⁷Co, ⁵⁸Co, ⁶⁰Co, ⁵¹Cr, ⁶¹Cu, ¹⁶⁹Er, ¹⁸F, ⁵²Fe, ⁵⁵Fe,⁵⁹Fe, ⁶⁷Ga, ¹²³I, ¹²⁵I, ¹³¹I, ¹¹¹In, ¹⁹²Ir, ⁸¹Kr, ¹⁷⁷Lu, ⁵²Mg, ¹³N,²²Na, ²⁴Na, ⁵⁷Ni, ¹⁵O, ³²P, ²⁰³Pb, ¹⁰³Pd, ⁸¹Rb, ⁷²Se, ⁷³Se, ⁷⁵Se, ¹⁵³Sm,⁸⁹Sr, ⁹⁹Sr, T, ⁹⁹Tc, ²⁰¹Tl, ¹⁶⁷Tm, ⁹⁰Y, ⁶²Zn, and ¹³³Xe. Examples ofreagents for radioisotope therapy and radioimmunotherapy include, butnot limited to, metaiodobenzylguanidine, oral iodine-131, hormone-boundlutetium-177 and yttrium-90, ibritumomab tiuxetan, tositumomabiodine-133, radioactive glass or resins, and radioactive nanoparticles.

The choice of the radiation therapy can be determined by taking intoconsideration various factors, including, e.g., the type, size, andlocation of the tumor, the age, weight, and condition of the subjectbeing treated. It is understood that the precise dose of the radiationand duration of treatment may vary with the age, weight, and conditionof the subject being treated, and may be determined empirically usingknown testing protocols or by extrapolation from in vivo or in vitrotest or diagnostic data. It is also understood that the total radiationdose required is often divided into two or more fractions, which areadministered over an extended period of time. It is further understoodthat for any particular individual, specific dosage regimens could beadjusted over time according to the individual need and the professionaljudgment of the person administering or supervising the administrationof the radiation.

In some embodiments, the total dose given in the radiotherapy is rangingfrom about 40 Gy to about 80 Gy. In certain embodiments, the total doseis divided into fractions and each fraction can be the same ordifferent. Each fraction ranges from about 0.5 Gy to about 50 Gy.

In some embodiments, the subject of the disclosed methods is furthertreated with an immunotherapy to enhance the abscopal effect. Forexample, dendritic cells (DCs) represent unique antigen-presenting cellscapable of activating T cells to both new and recall antigens. In fact,these cells are the most potent antigen-presenting cells. The goal of DCbased cancer immunotherapy is to use the cells to prime specificantitumor immunity through the generation of effector cells that attackand lyse tumors. Therefore, in some embodiments, the disclosed methodsfurther involve administering DCs to the subject. In some embodiments,the DCs are administered directly to the tumor lesion site(s) beingirradiated. In some embodiments, the DCs are administered systemicallyor to tumor site(s) in addition to or distinct from the sites beingirradiated.

Additional immunotherapeutic approaches include 1) use of exogenouscytokines to non-specifically stimulate the immune system's effectorcells to mount an anti-tumor response, 2) introduction ofimmuno-stimulatory antigens to precipitate a targeted immune response(i.e. active immunization or tumor vaccination), 3) exogenous expansionand reinfusion of tumor-specific immune cells (adoptive immunotherapy),4) immune system checkpoint modulation, and 5) use of cancer-killing andimmune system-stimulating modified viruses (oncolytic immunotherapy).Vaccination with telomerase vaccine (GV1001) can be combined with animmune adjuvant, e.g., granulocyte macrophage colony-stimulating factor(GM-CSF), and a cycle of gemcitabine chemotherapy.

Immunostimulatory cytokines include interferon alpha (IFN-α) andinterleukin-2 (IL-2). IFN-α directly inhibits tumor cell proliferation,enhances innate & adaptive immunity, facilitates tumor antigenrecognition via enhanced MHC I receptor expression, represses oncogenesand induces tumor suppressor gene expression, and inhibits angiogenesis.IL-2 activates B, T, & NK cells, and facilitating cytolytic destructionof tumor cells

Anticancer vaccines can facilitate tumor antigen recognition and asubsequent anti-tumor immune response by artificially introducingtumor-associated antigens to the body, or cellular equipment that canhelp expose those already present. Artificially introduced antigens cantake the form of peptide fragments, whole proteins, cell lysates orwhole cells. For example, telomerase is highly expressed in essentiallyall cancer forms, while the expression in normal tissues is restricted.Moreover, telomerase activity is considered indispensable for tumorimmortalization and growth. Human telomerase reverse transcriptase(hTERT), the rate-limiting subunit of the telomerase complex, istherefore an attractive target for cancer vaccination. GV1001, a peptidevaccine representing a 16-aa hTERT sequence, binds multiple HLA class IImolecules and harbors putative HLA class I epitopes. The peptide maytherefore elicit combined CD4/CD8 T-cell responses, considered importantto initiate tumor eradication and long-term memory.

Adoptive cell therapy (ACT) involves harvesting autologous lymphocytesfrom a patient's tumor or peripheral blood, expanding them and possiblymodifying them in-vitro to express tumor-associated antigen receptors orsecrete specific cytokines, and reintroducing them back into the host.The adoptive transfer of autologous tumor infiltrating lymphocytes (TIL)or in vitro re-directed peripheral blood mononuclear cells has been usedto successfully treat patients with advanced solid tumors, includingmelanoma and colorectal carcinoma, as well as patients withCD19-expressing hematologic malignancies.

Immunomodulatory monoclonal antibody (mAb) therapies include cytotoxicT-Lymphocyte Antigen-4 (CTLA-4) inhibition (e.g., ipilimumab),Programmed Death-1 (PD-1) inhibition (e.g., nivolumab andpembrolizumab), CD40 agonism, OX40 agonism, Lymphocyte Activation Gene-3(LAG-3) and T cell Immunoglobulin Mucin-3 (TIM-3) inhibition, andToll-like receptor agonists. CTLA-4 is a T cell receptor that naturallyinteracts with B7-1 (CD-80) and B7-2 (CD-86) on the surface of antigenpresenting cells, thereby down-regulating the T cell response andavoiding potential autoimmune damage. A costimulatory T cell surfaceprotein, CD-28, on the other hand, competes with CTLA-4, albeit withless affinity, for interaction with B7-1 and B7-2, activating the Tcell. Blocking CTLA-4 thereby allows CD-28 to interact with B7-1 andB7-2, enhancing the body's cellular immune response and ability toeradicate tumor cells. For poorly immunogenic tumors, CTLA-4 blockademay be effective if used in combination with vaccination with irradiatedtumor cells modified to produce GM-CSF.

PD-1 receptor is expressed on B, T, and NK cells, and interacts withProgrammed Death Ligands-1 and -2 (PDL-1 and -2), often subversivelyexpressed on melanoma cells, to induce T cell exhaustion anddown-regulate the immune response. By blocking PD-1, these medicationsfacilitate a more vigorous anti-tumor cellular immune response. CD40 isa costimulatory receptor of the tumor necrosis factor (TNF) familynormally expressed on a variety of cells including dendritic cells andmacrophages. Interaction with its ligand plays a key role in priming andproliferation of antigen-specific CD4 T cells. When expressed on tumorcells, its stimulation results in apoptosis. Thus, CD40-stimulating mAbs(e.g., CD-870873) have direct anti-tumor activity and induce tumorantigen-specific T cell responses. LAG-3 is a transmembrane proteinexpressed on T regulatory (T reg) cells that binds MHC II, oftenexpressed on melanoma cells, thereby enhancing T reg activity,negatively regulating the cellular immune response, and protectingmelanoma cells from apoptosis. Blocking LAG-3 could thus help the bodyfight tumor cells on two fronts. Another class of immunomodulators actupon TLRs, a group of cell-surface receptors found on sentinel immunecells like dendritic cells and macrophages that naturally activate aninnate immune response upon contact with characteristic pathogen-relatedantigens. Topical treatment of melanoma with Imiquimod (IMQ), a TLR-7agonist, has been shown to facilitate 1) tumor infiltration with immuneeffector cells such as activated, cytotoxic plasmacytoid DCs, 2) a typeI IFN response, 3) anti-angiogenic defenses, and in some cases result incomplete tumor regression.

The blockade of TGF-β by anti-TGF-β antibody can synergistically enhancetumor vaccine efficacy, which is mediated by CD8+ T cells. For example,fresolimumab is an antibody capable of neutralizing all human isoformsof transforming growth factor beta (TGFβ) and has demonstratedanticancer activity.

Generating optimal “killer” CD8 T cell responses also requires T cellreceptor activation plus co-stimulation, which can be provided throughligation of tumor necrosis factor receptor family members, includingOX40 (CD134) and 4-1BB (CD137). OX40 is of particular interest astreatment with an activating (agonist) anti-OX40 mAb augments T celldifferentiation and cytolytic function leading to enhanced anti-tumorimmunity against a variety of tumors.

Numerous anti-cancer drugs are available for combination with thepresent method and compositions. The following is a non-exhaustive listsof anti-cancer (anti-neoplastic) drugs that can be used in conjunctionwith irradiation: Acivicin; Aclarubicin; Acodazole Hydrochloride;AcrQnine; Adozelesin; Aldesleukin; Altretamine; Ambomycin; AmetantroneAcetate; Aminoglutethimide; Amsacrine; Anastrozole; Anthramycin;Asparaginase; Asperlin; Azacitidine; Azetepa; Azotomycin; Batimastat;Benzodepa; Bicalutamide; Bisantrene Hydrochloride; Bisnafide Dimesylate;Bizelesin; Bleomycin Sulfate; Brequinar Sodium; Bropirimine; Busulfan;Cactinomycin; Calusterone; Caracemide; Carbetimer; Carboplatin;Carmustine; Carubicin Hydrochloride; Carzelesin; Cedefingol;Chlorambucil; Cirolemycin; Cisplatin; Cladribine; Crisnatol Mesylate;Cyclophosphamide; Cytarabine; Dacarbazine; Dactinomycin; DaunorubicinHydrochloride; Decitabine; Dexormaplatin; Dezaguanine; DezaguanineMesylate; Diaziquone; Docetaxel; Doxorubicin; Doxorubicin Hydrochloride;Droloxifene; Droloxifene Citrate; Dromostanolone Propionate; Duazomycin;Edatrexate; Eflomithine Hydrochloride; Elsamitrucin; Enloplatin;Enpromate; Epipropidine; Epirubicin Hydrochloride; Erbulozole;Esorubicin Hydrochloride; Estramustine; Estramustine Phosphate Sodium;Etanidazole; Ethiodized Oil I 131; Etoposide; Etoposide Phosphate;Etoprine; Fadrozole Hydrochloride; Fazarabine; Fenretinide; Floxuridine;Fludarabine Phosphate; Fluorouracil; Flurocitabine; Fosquidone;Fostriecin Sodium; Gemcitabine; Gemcitabine Hydrochloride; Gold Au 198;Hydroxyurea; Idarubicin Hydrochloride; Ifosfamide; Ilmofosine;Iproplatin; Irinotecan Hydrochloride; Lanreotide Acetate; Letrozole;Leuprolide Acetate; Liarozole Hydrochloride; Lometrexol Sodium;Lomustine; Losoxantrone Hydrochloride; Masoprocol; Maytansine;Mechlorethamine Hydrochloride; Megestrol Acetate; Melengestrol Acetate;Melphalan; Menogaril; Mercaptopurine; Methotrexate; Methotrexate Sodium;Metoprine; Meturedepa; Mitindomide; Mitocarcin; Mitocromin; Mitogillin;Mitomalcin; Mitomycin; Mitosper; Mitotane; Mitoxantrone Hydrochloride;Mycophenolic Acid; Nocodazole; Nogalamycin; Ormaplatin; Oxisuran;Paclitaxel; Pegaspargase; Peliomycin; Pentamustine; Peplomycin Sulfate;Perfosfamide; Pipobroman; Piposulfan; Piroxantrone Hydrochloride;Plicamycin; Plomestane; Porfimer Sodium; Porfiromycin; Prednimustine;Procarbazine Hydrochloride; Puromycin; Puromycin Hydrochloride;Pyrazofurin; Riboprine; Rogletimide; Safmgol; Safingol Hydrochloride;Semustine; Simtrazene; Sparfosate Sodium; Sparsomycin; SpirogermaniumHydrochloride; Spiromustine; Spiroplatin; Streptonigrin; Streptozocin;Strontium Chloride Sr 89; Sulofenur; Talisomycin; Taxane; Taxoid;Tecogalan Sodium; Tegafur; Teloxantrone Hydrochloride; Temoporfin;Teniposide; Teroxirone; Testolactone; Thiamiprine; Thioguanine;Thiotepa; Tiazofurin; Tirapazamine; Topotecan Hydrochloride; ToremifeneCitrate; Trestolone Acetate; Triciribine Phosphate; Trimetrexate;Trimetrexate Glucuronate; Triptorelin; Tubulozole Hydrochloride; UracilMustard; Uredepa; Vapreotide; Verteporfin; Vinblastine Sulfate;Vincristine Sulfate; Vindesine; Vindesine Sulfate; Vinepidine Sulfate;Vinglycinate Sulfate; Vinleurosine Sulfate; Vinorelbine Tartrate;Vinrosidine Sulfate; Vinzolidine Sulfate; Vorozole; Zeniplatin;Zinostatin; Zorubicin Hydrochloride.

The term “abscopal effect” refers to a phenomenon in the treatment ofmetastatic cancer where localized irradiation of a tumor causes not onlya shrinking of the irradiated tumor but also a shrinking of tumorsoutside the irradiated area.

The term “subject” refers to any individual who is the target ofadministration or treatment. The subject can be a vertebrate, forexample, a mammal. Thus, the subject can be a human or veterinarypatient. The term “patient” refers to a subject under the treatment of aclinician, e.g., physician.

The term “treatment” refers to the medical management of a patient withthe intent to cure, ameliorate, stabilize, or prevent a disease,pathological condition, or disorder. This term includes activetreatment, that is, treatment directed specifically toward theimprovement of a disease, pathological condition, or disorder, and alsoincludes causal treatment, that is, treatment directed toward removal ofthe cause of the associated disease, pathological condition, ordisorder. In addition, this term includes palliative treatment, that is,treatment designed for the relief of symptoms rather than the curing ofthe disease, pathological condition, or disorder; preventativetreatment, that is, treatment directed to minimizing or partially orcompletely inhibiting the development of the associated disease,pathological condition, or disorder; and supportive treatment, that is,treatment employed to supplement another specific therapy directedtoward the improvement of the associated disease, pathologicalcondition, or disorder.

The term “neoplastic cell” or “neoplasm” refers to a cell undergoingabnormal cell proliferation (“neoplasia”). The growth of neoplasticcells exceeds and is not coordinated with that of the normal tissuesaround it. The growth typically persists in the same excessive mannereven after cessation of the stimuli, and typically causes formation of atumor. Neoplasms may be benign, premalignant, or malignant.

The term “cancer” or “malignant neoplasm” refers to a cell that displaysuncontrolled growth, invasion upon adjacent tissues, and oftenmetastasis to other locations of the body.

The term “tumor” refers to an abnormal mass of tissue containingneoplastic cells.

The term “metastasis” refers to the spread of malignant tumor cells fromone organ or part to another non-adjacent organ or part. Cancer cellscan “break away,” “leak,” or “spill” from a primary tumor, enterlymphatic and blood vessels, circulate through the bloodstream, andsettle down to grow within normal tissues elsewhere in the body. Whentumor cells metastasize, the new tumor is called a secondary ormetastatic cancer or tumor.

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

EXAMPLES

As disclosed herein, the key to inducing a patient-specific abscopaleffect is determining the interconnectivity of metastatic nodules andhost circulatory system through integration of radiological scans andlaboratory tests with quantitative modeling. Disclosed is an integrativeframework that translates personalized data into a ‘virtual patient’.Patient-specific treatment simulations can then be performed to predictpersonalized outcomes (FIG. 2). A preliminary framework designsuccessfully reproduced the clinical outcome of one metastatic melanomapatient. This approach can be further developed, calibrated, andvalidated with samples of patients with different clinical responses.

Example 1 Quantifying T Cell Trafficking to Identify Patient-SpecificIrradiation Targets that Trigger Abscopal Responses

Equations

Metastatic cancer is considered with N distinct tumors located indifferent organs. The cancer population at each metastatic site,C_(i)(t), is assumed to follow logistic growth with site dependentcarrying capacity, K_(i), and growth rate, r_(i), modulated by thepredation of immunocompetent effector cells, E_(i)(t). The equationgoverning each metastatic site growth is

$\begin{matrix}{\frac{{dC}_{i}}{dt} = {{r_{i}{C_{i}\left( {1 - \frac{C_{i}}{K_{i}}} \right)}} - {{apE}_{i}{C_{i}.}}}} & \left. A \right)\end{matrix}$

A detailed description of all variables and rate constants with specificvalues can be found in Table 1.

TABLE 1 Parameter values for the differential part of the model,equations (A) and (B). Parameter Value Unit Description r 0.188 1/dayMaximal tumor growth rate K 531.91 × 10⁶   cells Carrying capacity a0.139 × 10⁻⁶ 1/day/cells T cell - cancer cell interactions constant p0.998 non- Probability that during the interaction dimensional between Tcell and cancer cell the later will be killed λ 0.591 1/day Effectorcells decay rate E*  0.3 × 10⁶ cells Physiological level of effectorcells f 0.525 if t > 28 days 1/day/cells Magnitude of immune system and0 otherwise stimulation by the presence of cancer cells g 0.161 × 10⁶  cells Immune stimulation damping coefficient NOTE: C(t) measures cellnumber, but in the T cell trafficking part of the model its value isused in terms of tumor volume in milliliters according to the formulaV(C(t)) = C(t) × (4/3 π r³) × 10⁻¹² mL, where r is the diameter of thecell assumed to be equal 10 micrometers.

Effector cells are recruited endogenously as well as in relation totumor burden, and undergo spontaneous decay or exhaust from interactionswith cancer cells. Cells that are recruited in response to the tumorpresence are mainly the cytotoxic T lymphocytes, key component of theadaptive part of the immune system. The equation governing thepopulation of tumor infiltrating effector cells at each of themetastatic sites is

$\begin{matrix}{{\frac{{dE}_{i}}{dt} = {{\lambda \left( {T^{*} - E_{i}} \right)} - {{a\left( {1 - p} \right)}E_{i}C_{i}} + {\sum\limits_{j = 1}^{N}\; {{\omega_{ij}\left( \overset{\rightarrow}{C} \right)}\frac{{fC}_{j}}{g + C_{j}}E_{j}}}}},} & \left. B \right)\end{matrix}$

where functions ω_(ij)(C₁, . . . , C_(N)) describe the probabilitiesthat cytotoxic T cells activated at site j will infiltrate the ith tumorsite. After being activated in the tumor draining lymph node, T cellstravel through the lymphatic system, enter the blood circulation, andtravel in cycles with blood through the system of arteries, capillariesand veins. To quantify T cell movement in the blood four majorcoarse-grain flow compartments were distinguished: pulmonary circulation(LU); gastro-intestinal tract and spleen (GIS); liver (LI); and allother organs in the systemic circulation (SO). The distinctconsideration of LU, GIS, and LI is important as venous blood from GISflows through LI through the hepatic portal vein before gettingre-oxygenated in LU (FIG. 13A). T cell trafficking between compartmentsis based on the anatomy with rates being equal to physiological valuesof blood flow fractions (BFFs, % of cardiac output reaching to thecompartment). As described herein, BFFs for compartments (e.g., LU, LI,GIS, SO compartments), as well as BFFs for individual organs can beobtained/calculated according to techniques known in the art. Thisdisclosure contemplates that BFFs can be stored in the memory of acomputing device (e.g., the computing device of FIG. 19). For example,the BFFs can optionally be stored in a table and references as needed.H_(compartment) is denoted as the probability that the T cell will beabsorbed by one of tumor-harboring tissues after entering a givencompartment (FIG. 13B), i.e. H_(compartment)=ΣP_(i), where P_(i) is theprobability that the T cell will infiltrate ith tumor site in a givencompartment. The probability of T cell absorption by a given compartmentwas calculate using a Markov Chain approach

$P_{absorption} = {\frac{1}{\Delta}\left\{ \begin{matrix}H_{LU} & {{{at}\mspace{14mu} {LU}\mspace{14mu} {compartment}},} \\{{H_{LI}\left( {1 - H_{LU}} \right)}\left( {{BFF}_{LI} + {{BFF}_{GIS}\left( {1 - H_{GIS}} \right)}} \right.} & {{{at}\mspace{14mu} {LI}\mspace{14mu} {compartment}},} \\{H_{GIS}{{BFF}_{GIS}\left( {1 - H_{LU}} \right)}} & {{{at}\mspace{14mu} {GIS}\mspace{14mu} {compartment}},} \\{H_{SO}{{BFF}_{SO}\left( {1 - H_{LU}} \right)}} & {{{at}\mspace{14mu} {SO}\mspace{14mu} {compartment}},}\end{matrix} \right.}$

where Δ is a normalizing constant, i.e. such that the sum of absorptionprobabilities over all four compartments is equal to one. T cell decayin the blood system was not consider and, thus each T cell will beeventually absorbed in one of the compartments, with the average numberof systemic circulation cycles before absorption equal to

$\begin{matrix}{N_{cycles} = {\frac{1}{\Delta} = {\quad\frac{(1)}{\begin{matrix}{H_{LU} + {\left( {1 - H_{LU}} \right)\left\lbrack {{H_{LI}\left( {{BFF}_{LI} + {{BFF}_{GIS}\left( {1 - H_{GIS}} \right)}} \right)} +} \right.}} \\{{H_{GIS}{BFF}_{GIS}} + {H_{SO}B}}\end{matrix}}}}} & \left. C \right)\end{matrix}$

It was assumed that the probability of T cell infiltrating ith tumorsite, P_(i), is equal to the probability that the T cell will flowthrough the tumor site multiplied by the probability of extravasationfrom blood to the tissue, h. The former was approximated using therelative blood flow through a specific tumor bearing organ (e.g., aratio of BFF_(organ) to BFF_(compartment)) multiplied by the fraction oforgan (e.g., a ratio of V^(i) to V^(i) _(organ)) taken and, thus, theequation describing P_(i) is

$P_{i} = {h \times \frac{{BFF}_{organ}^{i}}{{BFF}_{compartment}^{i}} \times {\frac{V^{i}}{V_{organ}^{i}}.}}$

The volume of a tumor (V^(i)) can be determined from radiologicalimage(s) of the subject, for example, using image processing techniquesknown in the art including, but not limited to, volume rendering.Additionally, the volume of the tumor-bearing organ (V^(i) _(organ)) cansimilarly be determined from radiological image(s) of the subject. Itshould be understood that determination of the volume of thetumor-bearing organ from radiological image(s) of the subject willaccount for subject-specific differences in volume. Alternatively oradditionally, the volume of the tumor-bearing organ (V^(i) _(organ)) canbe the average volume of a tumor-bearing organ as known in the art asdescribed herein. This disclosure contemplates that organ volumes can bestored in the memory of a computing device (e.g., the computing deviceof FIG. 19). For example, the average organ volumes can optionally bestored in a table and references as needed. For example, in PET imagesgross tumor volumes can by automatically delineated using a segmentationalgorithm based on the measured signal-to noise ratio (Daisne J F, etal. Radiother Oncol. 2003 (69): 247-150).

Experimental studies clearly show that during the activation process inthe lymph node T cells are programmed to express homing moleculesspecific to the site of the immunization (Mikhak Z, et al. J Exp Med.2013 210(9):1855-69; Calzascia T, et al. Immunity. 2005 22(2):175-84).Thus it was assumed that h=h_(a) if the T cell was activated in thegiven organ, and h=h_(n) otherwise (1≧h_(a)>h_(n)). Probabilistic modeldefined above allows to calculate functions ω_(ij)(C₁, . . . , C_(N)) inthe effector cells dynamics equation (B) for different geographicdistribution of metastatic disease.

Materials and Methods

The different components of the mathematical framework were calculatedor solved numerically in MATLAB (www.mathworks.com).

Model Parameters Estimation

The gastro-intestinal tract consist mainly of stomach, esophagus,intestine and pancreas, with physiological blood flow fractions (BFFs)of 1%, 16% and 1%, respectively (Valentin J. Annals of the ICRP. 200232(3-4):1-277). BFF to the spleen is estimated to be 3% (Valentin J.Annals of the ICRP. 2002 32(3-4):1-277), which together yieldsBFF_(GIS)=21%. It is estimated that the internal mammalian artery withthe average blood flow of 59.9 mL/min, provides about 60% of breastblood supply. With an average cardiac output of 300 L/h (Abduljalil K,et al. Clin Pharmacokinet. 2012 51(6):365-96), BFF to the breast(BFF_(breast)) was estimated to be 2%. BFF to the kidney (BFF_(kidney))was estimated to be 8.5% (Valentin J. Annals of the ICRP. 200232(3-4):1-277).

In a study performed by Mikhak et al. (Mikhak Z, et al. J Exp Med. 2013210(9):1855-69), T cells isolated from mice transgenic for the TCRrecognizing ovalbumin (OVA, antigen) were activated in vitro withdendritic cells (DCs) isolated from different mouse tissues includinglung, thoracic lymph nodes and skin. Populations of activated T cellswere then injected into naïve mice and challenged with aerosolized OVA.24 h after the last challenge mice were sacrificed and lung tissueharvested. The number of T cells measured was about 3 times largercompared to other groups when T cells where activated with lung DSc.Thus, the extravasation probability of T cell to the tissue ofactivation (h_(a)) was estimate to be three times larger thanextravasation into non-activation tissue sites (h_(n); h_(n)/h_(a)=⅓).Values of other parameters associated with T cell trafficking, i.e.those that are necessary to calculate values of ω_(ij)(C₁, . . . ,C_(N)), were taken from literature and are summarized in Table 2.

TABLE 2 Parameter values for the T cell trafficking part of the model.Parameter Value Description Reference BFF_(LI) 6.5% Blood flow fractionto liver Valentin J. Annals of the ICRP. 2002 32(3-4): 1-277 BFF_(GIS) 21% Blood flow fraction to estimated gastro-intestinal tract and spleenBFF_(SO) 72.5%  Blood flow fraction to SO by definition = 100% −BFF_(LI) − BFF_(GIS) compartment BFF_(breast)   2% Blood flow fractionto the estimated breast BFF_(kidney) 8.5% Blood flow fraction to theValentin J. Annals of the ICRP. 2002 kidney 32(3-4): 1-277 V_(liver)1493 mL Average liver volume Henderson J M, et al. Radiology. 1981141(2): 525-7 V_(breast)  500 mL Average breast volume Abduljalil K, etal. Clin Pharmacokinet. 2012 51(6): 365-96 V_(lungs) 3679 mL Averagelung volume Puybasset L, et al. Am J Respir Crit Care Med. 1998 158(5 Pt1): 1644-55 V_(kidney)  249 mL Average kidney volume Poggio E D, et al.Am J Transplant. 2006 6(3): 616-24

Virtual Case Studies and Immunogenicity Quantification

C cohort was create of 40 virtual metastatic patients with arbitrarycombinations of breast, liver, kidney and lung metastases of randomsizes between 50 and 300 cc. Systemic T cells trafficking wasinvestigate for different sites of T cell activation via localradiotherapy with fixed dose to different individual metastatic sites.The T cells dissemination quality for different sites of activation wasevaluated by comparing the values of the entropy of established homingdistribution scaled by the maximum attainable entropy

$\begin{matrix}{{S_{i} = {\left( {\sum\limits_{j = 1}^{N}\; {P_{ij}\ln \; p_{ji}}} \right)/\left( {N\; \ln \; \frac{1}{N}} \right)}},} & \left. D \right)\end{matrix}$

where i is the site of activation, and p_(ij) is the probability that Tcell activated at site i will infiltrate tumor at site j. Theimmunogenicity index, reminiscent of the probability of triggering anabscopal effect, was define by additionally taking into account the sizeof the tumor relative to other sites

$\begin{matrix}{I_{i} = {S_{i}{\frac{V_{i}}{\max \left( {V_{1},\ldots \mspace{14mu},V_{N}} \right)}.}}} & \left. E \right)\end{matrix}$

Tumor size plays a crucial role as irradiation of larger tumors leads tomore cells undergoing immunogenic cell death, which translates intolocal immune activation. The maximum immunogenicity index of one (1) canonly be achieved theoretically if the largest tumor is treated and thedistribution of activated T cells was uniform between the metastaticsites. For expected non-uniform distributions of activated T cells,however, the tumor size alone is insufficient to predict immunogenicityindices.

Simulation of Experimental Metastatic Disease Progression

Breast cancer growth was initiated with 0.5×10⁶ cancer cells and tumorgrowth simulated. After 200 days the onset of a metastasis was simulatedby initiating a population of 0.5×10⁶ cancer cells in the lung, andgrowth of both tumor sites simulated for another 200 days. Forillustration purpose, the growth rate of the lung tumor was assumed tobe twice as fast as the breast tumor, what might reflect better oxygenavailability in the lung. Extravasation probabilities h_(a) and h_(n)were assumed to be equal 0.6 and 0.2, respectively.

Simulation of Primary Tumor Removal

After simulating the primary tumor growth in the breast and furtherprogression of the metastatic site in the lung we simulate completesurgical removal of the primary breast tumor by instantaneously removingboth cancer cells and T cells populations present in the breast.Parameters describing dynamics of the lung metastasis remain unchanged.

Results

Variation in Immunogenicity Between Metastatic Sites

A detailed analysis is provided of the first out of 40 generated virtualcase studies, which comprises of breast (113 cc), liver (220 cc) andlung (270 cc) metastases. FIG. 14 shows the distribution of T cells foractivation in breast, liver and lung, respectively, for different valuesof parameters h_(a)=[0,1] and h_(n)/h_(a)=[0,1]. Simulations reveal thatthe actual extravasation probability at the tissue of activation has anegligible influence on the systemic T cell distribution. However, theratio of extravasation probabilities at non-activation sites versusactivation sites, h_(n)/h_(a), significantly determines activated T celldistribution regardless of activation site (FIG. 14). Intuitively, ifh_(n)/h_(a)=0, T cell are unable to extravasate in any site other thantissue of activation, and no systemic response is possible. On the otherhand, if extravasation occurs at all sites at equal strength (i.e.,h_(n)/h_(a)=1), T cell distribution is identical regardless of tissue ofactivation. However, the T cells dissemination patterns vary greatlydependent on sites of activation for the intermediate h_(n)/h_(a)values, including estimated h_(n)/h_(a)=⅓.

Given the complexity of the arterial tree, even flowing through specificsite is a relatively rare event. In addition, both, T cell homing cue haand its ratio to extravasation into distant tissue, h_(n)/h_(a),significantly impact the number of circulatory cycles the T cells willtraffic before extravasating at a tumor-harboring site (FIG. 14D). Itfollows from eqn. (C) that the average number of cycles can increasewithout any limits when one considers smaller and smaller values ofparameter h_(a). If h_(a)=1 and h_(n)/h_(a)=1, T cells will perform onaverage about 9 circulatory cycles with a blood recirculation time of 10to 25 seconds (Puskas Z, et al. Der Radiologe. 1996 36(9):750-7), whichtranslates to about 2 minutes. For lower values, h_(a)=0.05 andh_(n)/h_(a)=0, model suggests about 4500 circulatory cycles (up to about32 hours) before certain extravasation in the case of T cell activationin the breast.

Entropy comparison between T cell homing distributions (eqn. (D)) showsthat distribution of activated T cells closest to the uniform can beachieved after treating the breast tumor in this virtual patient example(FIG. 15A), regardless of extravasation probabilities h_(a) and h_(n).Targeting the lung tumor, however, yields a heavily skewed distributionamong the metastatic sites, with lung being the largest attractor giventhe large BFF to the lung. To calculate the immunogenicity index (eqn.(E)), tumor sizes need to be integrated. In the virtual patient example,the liver metastases has the highest immunogenicity index forh_(n)/h_(a) values between 15% and 60%, including the estimated value ofh_(n)/h_(a)=⅓ (FIG. 15B).

Sites having the highest immunogenicity index were further calculated inother virtual case studies for the estimated values of h_(n)/h_(a)=⅓ andh_(a)=0.6 (FIG. 15C). In a given patient specific setting, the largesttumor size or the combination of existing metastases alone are not thepredictive factors when one considers the probability of triggering thesystemic response. Indeed, in the case study No. 5, the much smallerbreast tumor (53 cc) had higher immunogenicity index than much largerkidney tumor (254 cc). Case studies 20 and 21 have the same combinationof metastatic sites, but the tumors with the highest immunogenicityindices are at different locations. Therefore, there is a need to applyproposed framework for every individual case separately.

Discussion

Transition from local to metastatic disease severely diminishes patientprognosis. 10-15% of breast cancer patients, the second most commoncancer diagnosed worldwide, will develop metastasis within 3 years ofdiagnosis (McGuire A, et al. Cancer Metastasis Rev. 2015 34(1):145-55).Tumors for which no systemic screening for early detection exists areoften diagnosed with metastatic diseases (Ovaries, lung), furtheremphasizing the urgent need to develop novel approaches that providesystemic cancer control with limited toxicity. Immunotherapy has beenshown to synergize with local radiation (Reits E A, et al. J Exp Med.2006 203(5):1259-71; Lugade A A, et al. J Immunol. 2005 174(12):7516-23;Vatner R E, et al. Front Oncol. 2014 4:325), which is currently exploredin more than 10 active clinical trials (Vatner R E, et al. Front Oncol.2014 4:325). However, understanding of the biological and physicalprinciples underlying the complex dynamic interplay of radiation andimmunotherapy, locally and especially systemically, is still in itsinfancy. Of fascinating interest are increasing case reports of abscopalresponses of metastatic tumors distant to the areas targeted byradiation (Antoniades J, et al. Int J Radiat Oncol Biol Phys. 19772(1-2):141-7; Wersall P J, et al. Acta Oncol. 2006 45(4):493-7; EhlersG, et al. Br J Radiol. 1973 46(543):220-2). Experiments were conductedto identify if different metastatic sites have different potentials toinduce a systemic response, and if mathematical modeling can be used toidentify the most promising treatment targets, either alone or incombination, on a per patient basis.

A systemic tumor-immune system interaction framework is proposed, whichaccounts for activated T cell trafficking through the host circulatorysystem. From the patient-specific distribution of the metastatic sites,which can be acquired from routinely taken PET/CT scans, combined withphysiological information about T cell trafficking, the distribution ofradiotherapy-facilitated activation of T cells for each metastatic site,either alone or in combination, can be estimated. Using a virtualpatient cohort the activated T cell distribution was dependent on (i)the geographic distribution of metastatic sites, (ii) the tumor volumeof each metastasis, and (iii) the site of activation. Integrating thosepatient-specific characteristics, the immunogenicity index can becalculated, which can support the clinical decision as to whichmetastatic site serves as the most promising local treatment target toinduce abscopal responses. Disclosed is a process to quantify how localtumor-immune interactions may propagate systemically and predictpatient-specific treatment targets to trigger abscopal effects.

Example 2 Systemic Interdependence of Metastatic Tumor Growth ThroughActivated T Cell Trafficking

For illustration purpose the established Kuznetsov model of localtumor-immune interactions was used with reported parameter values(Kuznetsov V A, et al. Math Comput Model. 2001 33(12-13):1275-87). Thismodule of the framework, however, is interchangeable for any tumorgrowth and immune modulation model (Example 3). In some embodiments, themodel may be calibrated with organ-specific tumor growth kinetics andimmune surveillance to fully integrate local and systemic dynamics andconfidently support personalized decision making in the clinic.

Simulation of primary tumor growth for 200 days show that a primarytumor can be modulated by cytotoxic immune surveillance, keeping thetumor in a dormant state significantly below the imposed carryingcapacity (FIG. 16A). The onset of metastatic site disrupts the dynamicequilibrium between T cells and cancer cells in the primary site. Beforethe immune response against the metastasis is established locally, someof the T cells that are generated in the primary breast tumor trafficand extravasate at the metastatic site, allowing for a transient escapeand progression of the primary tumor (FIG. 16B). After T cells activatedby the lung metastasis begin trafficking in the circulatory system, thetotal number of T cell increases and an increase in T cells surveillingthe breast cancer can be observed. However, because of the attainedequilibrium of homing distributions (FIGS. 16C and 16D), the lowerproportion of T cell penetrating the breast allows the tumor to attaindormancy with cell numbers significantly larger than pre-metastasisformation. Interestingly, the lung metastasis is also kept at a dormantstate despite its larger growth rate, mostly due T cells that weregenerated in the breast and trafficked to the lung. What is mostinteresting, because of the large proliferation rate, lung tumor seededalone would escape the immune surveillance and grow to imposed carryingcapacity value (simulations not shown). Thus, surgical removal of thebreast cancer, accompanied by removal of locally infiltrated T cells aswell as prevention of future T cells activated in the breast, leads to arapid progression of the lung metastasis and a substantial decrease ofeffector to cancer cells ratio in the lung (FIG. 17).

Example 3 Local Mathematical Model of Tumor-Immune Interactions

In some embodiments, a model of local tumor-immune interactions can beintegrated into the framework. Cell populations of both primary andmetastatic nodules exhibit heterogeneous immunogenicity [Tufail S, etal. Front Immunol. 4:254, 2013; Marte B. Nature. 501(7467):327, 2013].Stimulation of immune effector cells is counterbalanced bytumor-mediated recruitment of immunoregulators [Ye J, et al. Cancer Res.73(20):6137-48, 2013]. Immunotherapeutic injection of autologousdendritic cells transiently shifts the local immune profile in favor ofeffector cells [Ward S T, et al. The Lancet. 381:S113, 2013]. Localirradiation has been observed to induce a pro-inflammatory immuneresponse as well as to shift non-immunogenic populations into animmunogenic phenotype in animal experiments [Demaria S, et al. ClinCancer Res. 11(2 Pt 1):728-34, 2005] and exploratory clinical trials[Hiniker S M, et al. N Engl J Med. 366(21):2035-6, 2012]. For simplicityit is assumed that the tumor population is divided into immunogenic(T_(I)) and non-immunogenic (T_(N)) cells, and the immune system intoEffector (E) and Regulatory (R) cells. These complex local dynamics canbe converted in a differential equation model (FIG. 5). While thedynamics of this system are universal, transition rates and parametersare patient-specific. 17 patients (stage 2 soft-tissue sarcoma withoutmetastatic spread) were enrolled in a Moffitt clinical trial thatcombined intratumoral administration of dendritic cells and localfractionated external beam radiation to determine localizedradiation-immune system synergy [Finkelstein S E, et al. Immunotherapy.4(4):373-382, 2012]. Preliminary results indicate that the mathematicalmodel (FIG. 5) can reproduce tumor volume, T cell dynamics and treatmentoutcome for a responder and a non-responder from this patient cohort(FIG. 6).

To validate the model and derive statistically optimized parametercalibrations, patient data from all 17 patients in that clinical trial[Finkelstein S E, et al. Immunotherapy. 4(4):373-382, 2012] areevaluated. To achieve this, a genetic algorithm is deployed to fit themodel to the available sequential measurements of tumor volume and CD3,CD 4 and CD8 counts for each patient. Genetic algorithms are establishedto explore large parameter spaces and compare simulation results todesired outcomes. The genetic algorithm is initialized with a population(n=1000) of random parameter values for the mathematical model.Parameter combinations that yield the smallest deviation from theclinical data forms the input population for the next iteration ofsimulations (‘genetic selection’), complemented by random combinationsof those successful parameter sets (‘crossover’) and random alterationsin single parameter values (‘mutations’). Through many iterations ofthis simulation-selection-modulation approach, parameter combinationsthat best describe patient response forms a ‘virtual patient cohort’.

Example 4 Whole Body Personalized Metastatic-Lymphatic InterconnectedNetwork Model

Diagnostic positron emission tomography (PET) scans or computertomography thorax, abdomen, pelvis (CT TAP) scans are available forpatients. Theses scans are used to accurately register the geographiclocation of each tumor site and their distance to the host lymphaticsystem. Three-dimensional radiological data sets are volume rendered andregistered using scientific visualization software (Matlab, IDL, ImageJ)and image processing algorithms. The patient-specific geographicmetastatic disease distribution is mapped onto a virtual lymphaticnetwork to create a ‘virtual patient’ (FIG. 3). Lymphatic networkinterconnectivity with different metastatic sites is estimated from Tcell infiltration immune scores (CD3, CD8) [Galon J, et al. J TranslMed. 10:1, 2012] through immunohistochemistry on 80 primary andmetastatic frozen tumor samples from 20 patients in the Moffitt CancerCenter Total Cancer Care multidimensional data warehouse. Immune scoreis correlated with relative distance to lymph nodes to interconnecttumor sites with the lymphatic network.

Central to the radiation and immune system orchestrated abscopal effectare immune signals that flow through the lymphatic network. Immunesignals in each lymph node flow to adjacent lymph nodes as well as tonearby metastatic sites. The immune signal in each node can additionallybe modulated by local irradiation that initiates an ad hoc immuneresponse [Sharma A, et al. Clin Cancer Res. 19(17):4843-53, 2013]. Aquantitative model was derived to capture these multiscale lymphaticnetwork dynamics. The mathematical model allows tracking the spread ofimmune signals through the lymphatic network as a function of time andestimation of the global impact triggered by local perturbations.Preliminary simulations of immune signal propagation through thelymphatic network after local irradiation suggest a variableconnectivity of lymph nodes and thus variable systemic impact (FIG. 4).Serial complete blood count data after local dendritic cell injectionavailable from a clinical trial [Finkelstein S E, et al. Immunotherapy.4(4):373-382, 2012] are used to calibrate and validate the model.

Example 5 Integrate Local and Systemic Models and Validate with ClinicalOutcome

The local interaction model is combined with the whole body model tosimulate patient specific systemic response to local irradiation andimmunotherapy. Every cancerous lesion (primary tumor and metastaticnodules) dynamically interacts with a local immune system (Example 2;FIG. 5), and all lesions are interconnected through systemiccommunication (Example 1; FIG. 4). Each tumor experiences andcorresponds to local as well as global signals. Results of localinteractions are communicated through the metastatic-lymphatic networkand influence subsequent dynamics of all other metastases dependent ontheir respective connectivities. Local radiotherapy is simulatedindependently on each metastatic nodule and transiently induced localimmune response and systemic immune signal propagation is monitored.This gives a global impact index for each tumor side. Combined withobservations of immune response in distant metastases and subsequenttumor modulation, the model yields the abscopal effect likelihood forirradiation of each individual metastatic site (FIG. 7).

The ‘virtual patient’ framework successfully simulated the abscopaleffect for n=1 patient [Seung S K, et al. Sci Transl Med.4(137):137ra74, 2012]. For this patient, the model suggests that thetumor that received local irradiation in the clinic was the only lesionthat could trigger such a response. Irradiation of each other lesionwould have resulted in local tumor control but systemic diseaseprogression (FIG. 7). This suggests that careful selection ofimmuno-communicative ‘hub’ nodes holds the key to successful abscopaldisease control.

In a retrospective study of 20 patients, diagnostic PET or CT TAP scansare used to generate patient-specific interconnectedmetastatic-lymphatic network graphs. Immunohistochemistry on primary andmetastatic tumor sites for each patient provide local immuneinfiltration immune scores and in combination with serial complete bloodcounts suggest systemic immune signal flow. The actual clinicallyapplied treatments are simulated for that patient. Then using theavailable sequential radiological images that were obtained during thecourse of treatment (4-6 per annum per patient) personalized modelpredictions are calibrated and validated. Model predictions are comparedto patient outcome, in terms of treatment responder or non-responder.

A nice feature of the disclosed integrated approach is that for thepatients in the retrospective study that had progressive disease, it caninvestigate if an alternative local radiotherapy of single orcombinations of metastatic nodes could have triggered abscopal effects.The focus of this ‘virtual patient’ treatment design framework is onabscopal effects in metastatic renal cell carcinoma in line with theclinical expertise of the investigator team. The translation of thedeveloped modules to other metastatic diseases with reported abscopaleffects like metastatic melanoma, hepatocellular carcinoma and chroniclymphocytic lymphoma [Wersall P J, et al. Acta Oncol. 45(4):493-7, 2006;Postow M A, et al. N Engl J Med. 366(10):925-31, 2012; Ohba K, et al.Gut. 43(4):575-7, 1998] is straightforward and a natural extension ofour work here, but would need to be implemented in collaboration withclinical experts in those cancers.

Computing Device

It should be appreciated that the logical operations described hereinwith respect to the various figures may be implemented (1) as a sequenceof computer implemented acts or program modules (i.e., software) runningon a computing device, (2) as interconnected machine logic circuits orcircuit modules (i.e., hardware) within the computing device and/or (3)a combination of software and hardware of the computing device. Thus,the logical operations discussed herein are not limited to any specificcombination of hardware and software. The implementation is a matter ofchoice dependent on the performance and other requirements of thecomputing device. Accordingly, the logical operations described hereinare referred to variously as operations, structural devices, acts, ormodules. These operations, structural devices, acts and modules may beimplemented in software, in firmware, in special purpose digital logic,and any combination thereof. It should also be appreciated that more orfewer operations may be performed than shown in the figures anddescribed herein. These operations may also be performed in a differentorder than those described herein.

When the logical operations described herein are implemented insoftware, the process may execute on any type of computing architectureor platform. For example, referring to FIG. 19, an example computingdevice upon which embodiments of the invention may be implemented isillustrated. The computing device 1900 may include a bus or othercommunication mechanism for communicating information among variouscomponents of the computing device 1900. In its most basicconfiguration, computing device 1900 typically includes at least oneprocessing unit 1906 and system memory 1904. Depending on the exactconfiguration and type of computing device, system memory 1904 may bevolatile (such as random access memory (RAM)), non-volatile (such asread-only memory (ROM), flash memory, etc.), or some combination of thetwo. This most basic configuration is illustrated in FIG. 19 by dashedline 1902. The processing unit 1906 may be a standard programmableprocessor that performs arithmetic and logic operations necessary foroperation of the computing device 1900.

Computing device 1900 may have additional features/functionality. Forexample, computing device 1900 may include additional storage such asremovable storage 1908 and non-removable storage 1910 including, but notlimited to, magnetic or optical disks or tapes. Computing device 1900may also contain network connection(s) 1916 that allow the device tocommunicate with other devices. Computing device 1900 may also haveinput device(s) 1914 such as a keyboard, mouse, touch screen, etc.Output device(s) 1912 such as a display, speakers, printer, etc. mayalso be included. The additional devices may be connected to the bus inorder to facilitate communication of data among the components of thecomputing device 1900. All these devices are well known in the art andneed not be discussed at length here.

The processing unit 1906 may be configured to execute program codeencoded in tangible, computer-readable media. Computer-readable mediarefers to any media that is capable of providing data that causes thecomputing device 1900 (i.e., a machine) to operate in a particularfashion. Various computer-readable media may be utilized to provideinstructions to the processing unit 1906 for execution. Common forms ofcomputer-readable media include, for example, magnetic media, opticalmedia, physical media, memory chips or cartridges, a carrier wave, orany other medium from which a computer can read. Examplecomputer-readable media may include, but is not limited to, volatilemedia, non-volatile media and transmission media. Volatile andnon-volatile media may be implemented in any method or technology forstorage of information such as computer readable instructions, datastructures, program modules or other data and common forms are discussedin detail below. Transmission media may include coaxial cables, copperwires and/or fiber optic cables, as well as acoustic or light waves,such as those generated during radio-wave and infra-red datacommunication. Example tangible, computer-readable recording mediainclude, but are not limited to, an integrated circuit (e.g.,field-programmable gate array or application-specific IC), a hard disk,an optical disk, a magneto-optical disk, a floppy disk, a magnetic tape,a holographic storage medium, a solid-state device, RAM, ROM,electrically erasable program read-only memory (EEPROM), flash memory orother memory technology, CD-ROM, digital versatile disks (DVD) or otheroptical storage, magnetic cassettes, magnetic tape, magnetic diskstorage or other magnetic storage devices.

In an example implementation, the processing unit 1906 may executeprogram code stored in the system memory 1904. For example, the bus maycarry data to the system memory 1904, from which the processing unit1906 receives and executes instructions. The data received by the systemmemory 1904 may optionally be stored on the removable storage 1908 orthe non-removable storage 1910 before or after execution by theprocessing unit 1906.

Computing device 1900 typically includes a variety of computer-readablemedia. Computer-readable media can be any available media that can beaccessed by device 1900 and includes both volatile and non-volatilemedia, removable and non-removable media. Computer storage media includevolatile and non-volatile, and removable and non-removable mediaimplemented in any method or technology for storage of information suchas computer readable instructions, data structures, program modules orother data. System memory 1904, removable storage 1908, andnon-removable storage 1910 are all examples of computer storage media.Computer storage media include, but are not limited to, RAM, ROM,electrically erasable program read-only memory (EEPROM), flash memory orother memory technology, CD-ROM, digital versatile disks (DVD) or otheroptical storage, magnetic cassettes, magnetic tape, magnetic diskstorage or other magnetic storage devices, or any other medium which canbe used to store the desired information and which can be accessed bycomputing device 1900. Any such computer storage media may be part ofcomputing device 1900.

It should be understood that the various techniques described herein maybe implemented in connection with hardware or software or, whereappropriate, with a combination thereof. Thus, the methods andapparatuses of the presently disclosed subject matter, or certainaspects or portions thereof, may take the form of program code (i.e.,instructions) embodied in tangible media, such as floppy diskettes,CD-ROMs, hard drives, or any other machine-readable storage mediumwherein, when the program code is loaded into and executed by a machine,such as a computing device, the machine becomes an apparatus forpracticing the presently disclosed subject matter. In the case ofprogram code execution on programmable computers, the computing devicegenerally includes a processor, a storage medium readable by theprocessor (including volatile and non-volatile memory and/or storageelements), at least one input device, and at least one output device.One or more programs may implement or utilize the processes described inconnection with the presently disclosed subject matter, e.g., throughthe use of an application programming interface (API), reusablecontrols, or the like. Such programs may be implemented in a high levelprocedural or object-oriented programming language to communicate with acomputer system. However, the program(s) can be implemented in assemblyor machine language, if desired. In any case, the language may be acompiled or interpreted language and it may be combined with hardwareimplementations.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of skill in the artto which the disclosed invention belongs. Publications cited herein andthe materials for which they are cited are specifically incorporated byreference.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

1. A method for personalized treatment of a subject with a plurality oftumor lesions in two or more tumor bearing organs, comprising (a)determining the location and volume for each of the plurality of tumorlesions in the subject; (b) modeling the blood flow dynamics and T cellextravasation probabilities for each tumor lesion to predict homingdistribution of T cells activated at each tumor lesion; (c) calculatingan immunogenicity index value for each tumor lesion based on thepredicted homing distribution and volume of each tumor lesion; and (d)treating the tumor lesion(s) in the subject having the highestimmunogenicity index with a local therapy that induces immunogenic celldeath.
 2. The method of claim 1, wherein step (a) comprisesthree-dimensional radiological images of the subject registeringgeographic locations of each of the plurality of tumor lesions.
 3. Themethod of claim 2, wherein the radiological images comprise positronemission tomography (PET) scans, x-ray computerized tomography (CT),magnetic resonance imaging (MRI), nuclear magnetic resonance imaging(NMRI), magnetic resonance tomography (MRT), or a combination thereof.4. The method of claim 1, wherein homing distribution in step (b) ispredicted by a method that comprises: i. determining the volume of eachtumor lesion and the volume of its tumor bearing organ to identify theproportion of the blood flow to the organ that supplies the tumor; ii.determining a physiologic blood flow fraction for each tumor bearingorgan; iii. calculating for each tumor lesion an infiltrationprobability that predicts whether a T cell in circulation willinfiltrate the tumor lesion in a single circulatory cycle based on thetumor density of the tumor lesion, the physiologic blood flow fractionof the tumor lesion, and the extravasation probability for T cellsactivated in the organ of the tumor lesion, not activated in the organof the tumor lesion, or a combination thereof; iv. calculating for eachtumor lesion a homing probability that predicts the relative number ofactivated T cells that will home to the tumor lesion based on theinfiltration probabilities for each tumor lesion; and v. calculating foreach tumor lesion a homing distribution entropy value that predicts therelative distribution of T cells activated in the tumor lesion based onthe total number of tumor lesions and the calculated homing probabilityfor each tumor lesion.
 5. The method of claim 1, wherein theimmunogenicity index value predicts which tumor lesion has the highestlikelihood that its irradiation will induce an abscopal effect.
 6. Themethod of claim 1, wherein at least one of the tumor lesions is ametastatic tumor lesion.
 7. The method of claim 1, wherein the targetedtherapy comprises radiotherapy.
 8. The method of claim 7, wherein theradiotherapy is selected from the group consisting of fractionatedradiation therapy, hypofractionated radiation therapy, hyperfractionatedradiation therapy, single-dose irradiation, stereo tactic radiosurgery,and stereotactic body radiation therapy.
 9. The method of claim 1,wherein the targeted therapy comprises an ablative therapy.
 10. Themethod of claim 9, wherein the ablative therapy is selected from thegroup consisting of thermal ablation (radiofrequency ablation (RFA),microwave ablation, and non-invasive high intensity focused ultrasound(HIFU) ablation.
 11. The method of claim 1, further comprising treatingthe subject with an immunotherapy.
 12. The method of claim 11, whereinthe method comprises intratumoral injection of dendritic cells into thetumor lesion having the highest immunogenicity index.
 13. The method ofclaim 1, further comprising treating the subject with a chemotherapy.14. The method of claim 1, wherein at least one tumor lesion ispreselected for irradiation, wherein step (d) comprises treating thetumor lesion(s) having the highest immunogenicity index in view of thepreselected tumor lesion.
 15. The method of claim 1, wherein theimmunogenicity index value is further based on the doseability of thetumor lesion with the targeted therapy.
 16. A system for providing apersonalized treatment plan for a subject with a plurality of tumorlesions in two or more tumor bearing organs, comprising: a processor;and a memory operably coupled to the processor, the memory havingcomputer-executable instructions stored thereon that, when executed bythe processor, cause the processor to: determine a respective volume ofeach of the tumor lesions using at least one radiological image of thesubject; obtain a respective physiologic blood flow fraction associatedwith each of the tumor lesions; obtain a respective T cell extravasationprobability associated with each of the tumor lesions; calculate arespective homing distribution for each of the tumor lesions based onthe respective volume of each of the tumor lesions, the respectivephysiologic blood flow fraction associated with each of the tumorlesions, and the respective T cell extravasation probability associatedwith each of the tumor lesions; calculate a respective immunogenicityindex value for each of the tumor lesions based on the respectivevolumes of each of the tumor lesions and the respective homingdistributions for each of the tumor lesions; and provide arecommendation for treating one or more of the tumor bearing organs witha targeted therapy that induces immunogenic cell death based on therespective immunogenicity index values for each of the tumor lesions.17-29. (canceled)